A context for recruitment correlations: why marine fisheries biologists should still look for them

In many cases when ecologists want to investigate a process, they often look for the best system on which to conduct the research, "best" meaning that the possibility of discovering mechanisms is optimized or made easier in some way. In fisheries we do it backwards. The species and system are given to us by economics, and we then fly in the face of the difficult circumstances to find mechanisms that are elusive anyway. These difficult circumstances constitute in some sense the first set of statistical problems. Using examples from the Northeast Pacific, I review the characteristics of cohort time series that make some species more tractable; propose a conscious process of conceptualization to assist in the formulation of clear, germane hypotheses; highlight the contrast between modeling in the sense of statistical fitting versus simulation models of processes; explore how the first round of models integrates with the second round of planning for new data collection at sea and in the lab; and, finally, propose how to judge success in terms of an operational approach.     

An evaluation of the Olsen test as a measure of plant-available phosphorus in grassland soils derived from basalt parent material

Abstract. Anecdotal and circumstantial evidence have suggested that the Olsen test underestimates plant-available phosphorus (P) in basaltic soils in Northern Ireland. Therefore, the ability of this test to predict plant-available P in basaltic (and non-basaltic) soils was investigated by regressing Olsen-P data against herbage P indices calculated from plant tissue test data using the diagnosis and recommendation integrated system. The average Olsen-P concentration for a range of fields situated on basaltic soils was considerably lower than the average Olsen-P concentration for a range of fields situated on non-basaltic soils, and yet mean sward P status, as given by the herbage P indices, was similar for both groups of fields. Herbage P indices were also much better correlated with Olsen-P measurements in non-basaltic soils than in basaltic soils. Furthermore, at low Olsen-P values (≶9mgPL⁻¹) some swards on basaltic soils were genuinely deficient in P, while others were sufficient or even in surplus for this nutrient. The results confirm that Olsen-P is inadequate as a predictor of plant-available P in basaltic soils. It is concluded that an alternative soil test is needed to provide a reliable assessment of plant-available P in basaltic soils, to prevent overuse of fertilizer and manure P and to minimize the amounts of P entering local watercourses.     

Identification of the porcine cytomegalovirus major capsid protein gene.

A major capsid protein (MCP) gene homologue of porcine cytomegalovirus (PCMV) was identified. Sequence analysis indicated that the PCMV MCP gene is 4,026 nucleotides in length encoding a protein of 1,341 amino acid residues. The predicted molecular weight of the PCMV MCP is 151,456 Da, equivalent to those of other herpesvirus MCP counterparts. Phylogenetic analysis using herpesviral MCP gene sequences confirmed that PCMV is a betaherpesvirus with higher homology with human herpesvirus-6 and -7 than human and mouse cytomegaloviruses. The serum of pig experimentally infected with PCMV did not react with bacterially expressed MCP, suggesting that the PCMV MCP may not be related to the humoral immune response in the course of PCMV infection. Also, we established polymerase chain reaction (PCR) protocols using primers corresponding to MCP gene sequences for detection of PCMV infection. The PCR protocol would be effective for the diagnosis of slow-growing PCMV infection, for which traditional methods involving virus-isolation are not useful.     

Doxorubicin affects the cardiac muscarinic system in the rat.

During the study on the mechanism of doxorubicin-induced cardiotoxicity, we observed that a long incubation (4 hr) with doxorubicin reduced the maximal negative inotropic effects of a muscarinic receptor agonist, carbachol. The mechanism responsible for this doxorubicin-induced reduction of the efficacy of carbachol was examined in isolated guinea pig hearts. In isolated left atrial muscle preparations, 1 hr incubation with 100 microM doxorubicin caused a parallel right-ward shift of the concentration-response curves for carbachol, but a longer (4 hr) incubation with this agent (30, 100 or 200 microM), caused a significant reduction of the magnitude of the negative inotropic effect of carbachol in addition to the concentration-dependent parallel right-ward shift. The 4-hr incubation with these concentrations of doxorubicin also reduced the maximal negative inotropic effect of an adenosine A1 receptor agonist, R-phenylisopropyl adenosine (R-PIA), without affecting the potency of this agonist. Doxorubicin (1 to 100 microM) reduced [3H]quinuclidinyl benzilate (QNB) binding in a concentration dependent manner, but failed to alter [3HIR-PIA binding. The decrease in the magnitude of the maximal negative inotropic effect by doxorubicin was caused by changes in the muscarinic system at steps common to the transduction of muscarinic and adenosine A1 receptor mechanisms.     

The extent of genetic diversity among Vanilla species: Comparative results for RAPD and ISSR

Vanilla is a large genus of about 110 species in the orchid family (Orchidaceae), including the species Vanilla planifolia from which commercial vanilla flavoring is derived. Since most species of vanilla are considered rare and endangered there is an urgent need to conserve them through genetic analysis and propagation/conservation studies on this crop.The present study investigated the genetic diversity among nine leafy- and leaf-less Vanilla species employing 30 decamer RAPD primers and 10 ISSR primers. The species under study were diverse and displayed a range of variability (0–66% and 0–81% for RAPD and ISSR, respectively). A total of 154 RAPD polymorphic markers (83.24%, h = 0.378) and 93 ISSR polymorphic markers (86.11%, h = 0.363) were used to generate a genetic similarity matrix followed by the cluster analysis. Specific groupings were revealed by each cluster analysis with slight variation between two different markers. Among the nine species studied, V. planifolia, Vanilla aphylla and Vanilla tahitensis revealed very low level of variation within their collections, thus indicating a narrow genetic base. The large genetic distance of Vanilla andamanica from other species suggests its different origin. A close genetic affinity was observed between the pairs V. planifolia, V. tahitensis and Vanilla albida, V. aphylla. These are the first comparative results for RAPD and ISSR reporting inter-relationship among nine cultivated, wild and hybrid Vanilla species.     

Comparison of three in vitro techniques to estimate benzimidazole resistance in Haemonchus contortus of sheep

Three in vitro assays to detect benzimidazole resistance, namely, the egg-hatch assay, tubulin-binding assay, and a larval-development assay, were evaluated by estimating the level of benzimidazole resistance in three field isolates of Haemonchus contortus compared with a susceptible reference strain. Comparisons were also made with estimates of benzimidazole resistance of the three field strains obtained from an in vivo controlled anthelmintic efficacy test. All three in vitro tests showed similar, consistent results which also suggested greater sensitivity than the in vivo assay. These results indicate that selection of an in vitro technique to determine benzimidazole resistance should therefore be based on considerations other than precision, such as technical expertise, availability of equipment, cost and speed in which diagnosis is required.